Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 11 of 189
Found at i:3663272 original size:22 final size:22
Alignment explanation
Indices: 3663239--3663289 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
3663229 ACTTTTTTTA
3663239 ATTTT-AAAATATTTTAAAATT
1 ATTTTAAAAATATTTTAAAATT
*
3663260 ATTTTAAAAATATTTTAAATTT
1 ATTTTAAAAATATTTTAAAATT
*
3663282 TTTTTAAA
1 ATTTTAAA
3663290 TTTTTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTAAAAATATTTTAAAATT
Found at i:3663290 original size:11 final size:11
Alignment explanation
Indices: 3663272--3663296 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3663262 TTTAAAAATA
3663272 TTTTAAATTTT
1 TTTTAAATTTT
3663283 TTTTAAATTTT
1 TTTTAAATTTT
3663294 TTT
1 TTT
3663297 ATTTTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTAAATTTT
Found at i:3663293 original size:10 final size:10
Alignment explanation
Indices: 3663240--3663308 Score: 61
Period size: 10 Copynumber: 6.9 Consensus size: 10
3663230 CTTTTTTTAA
*
3663240 TTTTAAAATA
1 TTTTAAAATT
3663250 TTTTAAAATT
1 TTTTAAAATT
*
3663260 ATTTTAAAAATA
1 -TTTT-AAAATT
*
3663272 TTTTAAATTT
1 TTTTAAAATT
*
3663282 TTTTTAAATT
1 TTTTAAAATT
*
3663292 TTTT--TATT
1 TTTTAAAATT
3663300 TTTTAAAAT
1 TTTTAAAAT
3663309 AAAAATGGGC
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
8 7 0.15
10 27 0.57
11 8 0.17
12 5 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTTAAAATT
Found at i:3664290 original size:40 final size:39
Alignment explanation
Indices: 3664238--3664328 Score: 137
Period size: 40 Copynumber: 2.3 Consensus size: 39
3664228 CCTTTAGACA
* *
3664238 TTAAATTCTAATTTAACCTTTTCTTTAAAATCATAAATT
1 TTAAAATCTAATTTAACCTTTTCTTTAAAATCATAAATC
*
3664277 TTAAAATCTTAATTTAACCTTTTCTTTAAAATTATAAATC
1 TTAAAATC-TAATTTAACCTTTTCTTTAAAATCATAAATC
3664317 TTAAAATTCTAA
1 TTAAAA-TCTAA
3664329 CTCACTAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 7 0.15
40 38 0.81
41 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (39 bp):
TTAAAATCTAATTTAACCTTTTCTTTAAAATCATAAATC
Found at i:3669933 original size:43 final size:43
Alignment explanation
Indices: 3669886--3669972 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
3669876 TTCCTACCGT
*
3669886 TGGAAT-TGGCCTTCGGCTGTGGATATACAACAGTACTTGTAGA
1 TGGAATAT-GCCTTCGGCTGTGGATACACAACAGTACTTGTAGA
* * * *
3669929 TGGAATATGCCTTCGTCTGTGGGTGCACAGCAGTACTTGTAGA
1 TGGAATATGCCTTCGGCTGTGGATACACAACAGTACTTGTAGA
3669972 T
1 T
3669973 AGTAGTTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
43 37 0.97
44 1 0.03
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (43 bp):
TGGAATATGCCTTCGGCTGTGGATACACAACAGTACTTGTAGA
Found at i:3672542 original size:30 final size:30
Alignment explanation
Indices: 3672506--3672583 Score: 138
Period size: 30 Copynumber: 2.6 Consensus size: 30
3672496 ATTTTATTGC
*
3672506 TAATTTTTTTATTATTTTAAAGAGATTTGT
1 TAATTTTGTTATTATTTTAAAGAGATTTGT
*
3672536 TAATTTTGTTATTATTTTAGAGAGATTTGT
1 TAATTTTGTTATTATTTTAAAGAGATTTGT
3672566 TAATTTTGTTATTATTTT
1 TAATTTTGTTATTATTTT
3672584 TTATTGCTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (30 bp):
TAATTTTGTTATTATTTTAAAGAGATTTGT
Found at i:3701316 original size:31 final size:31
Alignment explanation
Indices: 3701281--3701339 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3701271 TTGGAGTAAA
*
3701281 TAGGGATAGTTTAGGTATTAAAAGTTAAGAG
1 TAGGGATAATTTAGGTATTAAAAGTTAAGAG
*
3701312 TAGGGGTAATTTAGGTATTAAAAGTTAA
1 TAGGGATAATTTAGGTATTAAAAGTTAA
3701340 TGGCAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (31 bp):
TAGGGATAATTTAGGTATTAAAAGTTAAGAG
Found at i:3704025 original size:6 final size:6
Alignment explanation
Indices: 3704014--3704038 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3704004 TCACCCACAA
3704014 AAACAC AAACAC AAACAC AAACAC A
1 AAACAC AAACAC AAACAC AAACAC A
3704039 CAGAGATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACAC
Found at i:3705122 original size:36 final size:36
Alignment explanation
Indices: 3705067--3705138 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
3705057 TCTGTCCATA
* * *
3705067 TGCGGTGTAACGGTTTTGATTCCTCCTAAAGGGAAT
1 TGCGGTGAAACGATCTTGATTCCTCCTAAAGGGAAT
3705103 TGCGGTGAAACGATCTTGATTCCTCCTAAAGGGAAT
1 TGCGGTGAAACGATCTTGATTCCTCCTAAAGGGAAT
3705139 CACATGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (36 bp):
TGCGGTGAAACGATCTTGATTCCTCCTAAAGGGAAT
Found at i:3705169 original size:133 final size:133
Alignment explanation
Indices: 3704931--3705175 Score: 357
Period size: 133 Copynumber: 1.8 Consensus size: 133
3704921 TTGTGTATAT
* * *
3704931 ATATGTGGTGTAACAGTCTTGATTCCTGCTAAAGGGAAGTGCTGTATAACGATCTTGATTCCTCC
1 ATATGCGGTGTAACAGTCTTGATTCCTCCTAAAGGGAAGTGCGGTATAACGATCTTGATTCCTCC
* * * **
3704996 TAAGGGGGATCGCATGAGCTGCATTTAAGTGAGTGTCTATCTACACGCGTGCTAGTCTTTTTCTG
66 TAAAGGGAATCACATGAGCTGCATTTAAGTGAGCATCTATCTACACGCGTGCTAGTCTTTTTCTG
3705061 TCC
131 TCC
* * *
3705064 ATATGCGGTGTAACGGTTTTGATTCCTCCTAAAGGGAATTGCGGTGA-AACGATCTTGATTCCTC
1 ATATGCGGTGTAACAGTCTTGATTCCTCCTAAAGGGAAGTGCGGT-ATAACGATCTTGATTCCTC
**
3705128 CTAAAGGGAATCACATGATTTGCATTTAAGTGAGCATCTATCTACACG
65 CTAAAGGGAATCACATGAGCTGCATTTAAGTGAGCATCTATCTACACG
3705176 TGCGTGAGAT
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
133 97 0.99
134 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (133 bp):
ATATGCGGTGTAACAGTCTTGATTCCTCCTAAAGGGAAGTGCGGTATAACGATCTTGATTCCTCC
TAAAGGGAATCACATGAGCTGCATTTAAGTGAGCATCTATCTACACGCGTGCTAGTCTTTTTCTG
TCC
Found at i:3710704 original size:78 final size:78
Alignment explanation
Indices: 3710605--3710843 Score: 388
Period size: 78 Copynumber: 3.1 Consensus size: 78
3710595 GTAGATCAGT
* * *
3710605 TGATGGCGCTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACTCTGGTGATACACCCAAGTCTA
1 TGATGTCGCTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTA
3710670 CCAAATCCAAGGA
66 CCAAATCCAAGGA
*
3710683 TGATGTCGCTTCAAAAATAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTA
1 TGATGTCGCTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTA
*
3710748 CCAAATCCGAGGA
66 CCAAATCCAAGGA
* * * *
3710761 GGATGTCACTTCAAAAGTAGGCAACAAATCCAAAAGTGGGGACACTGGTGACACACCCAAGTCTA
1 TGATGTCGCTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTA
*
3710826 CCAAATCCAAGAA
66 CCAAATCCAAGGA
3710839 TGATG
1 TGATG
3710844 ACAATGTTAA
Statistics
Matches: 148, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 148 1.00
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (78 bp):
TGATGTCGCTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTA
CCAAATCCAAGGA
Found at i:3716861 original size:68 final size:68
Alignment explanation
Indices: 3716786--3716921 Score: 238
Period size: 68 Copynumber: 2.0 Consensus size: 68
3716776 ACAAAATAAT
* *
3716786 AATAATAA-AATAACATCAAGTTTGTTTTATTAATCAAATGTTAGATTTTGTTACAACAATTAAT
1 AATAATAATAA-AACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAACAATTAAT
3716850 ACAA
65 ACAA
3716854 AATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATA
1 AATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATA
3716919 CAA
66 CAA
3716922 TTAATTCAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 63 0.97
69 2 0.03
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.38
Consensus pattern (68 bp):
AATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATA
CAA
Found at i:3716923 original size:9 final size:9
Alignment explanation
Indices: 3716909--3716952 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
3716899 TTTTGTTACA
3716909 ACAATTAAT
1 ACAATTAAT
3716918 ACAATTAAT
1 ACAATTAAT
*
3716927 TCAATT-A-
1 ACAATTAAT
3716934 ACAATTAAT
1 ACAATTAAT
3716943 ACAATTAAT
1 ACAATTAAT
3716952 A
1 A
3716953 ATTTGATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 5 0.16
8 2 0.06
9 24 0.77
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (9 bp):
ACAATTAAT
Found at i:3716939 original size:16 final size:16
Alignment explanation
Indices: 3716918--3716955 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3716908 AACAATTAAT
*
3716918 ACAATTAATTCAATTA
1 ACAATTAATACAATTA
3716934 ACAATTAATACAATTA
1 ACAATTAATACAATTA
*
3716950 ATAATT
1 ACAATT
3716956 TGATAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (16 bp):
ACAATTAATACAATTA
Found at i:3716980 original size:16 final size:16
Alignment explanation
Indices: 3716959--3717000 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
3716949 AATAATTTGA
*
3716959 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
3716975 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
3716991 TAGTTTTAAT
1 TAATTTTAAT
3717001 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:3718693 original size:16 final size:17
Alignment explanation
Indices: 3718672--3718710 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3718662 ATTTTATAGC
3718672 TTCAAT-CTTATTTTTT
1 TTCAATGCTTATTTTTT
3718688 TTCAATGCTTATTTTTT
1 TTCAATGCTTATTTTTT
3718705 TTCAAT
1 TTCAAT
3718711 TGATAAACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.21, C:0.13, G:0.03, T:0.64
Consensus pattern (17 bp):
TTCAATGCTTATTTTTT
Found at i:3721890 original size:26 final size:26
Alignment explanation
Indices: 3721871--3721928 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
3721861 CCCGATATAT
3721871 GGCTCTTCATGAGCTTCCCGATTAAA
1 GGCTCTTCATGAGCTTCCCGATTAAA
** ** *
3721897 GGCTCTTTGTGAGCTTCCTAATTAAT
1 GGCTCTTCATGAGCTTCCCGATTAAA
3721923 GGCTCT
1 GGCTCT
3721929 CCGGAGCTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (26 bp):
GGCTCTTCATGAGCTTCCCGATTAAA
Found at i:3734803 original size:12 final size:12
Alignment explanation
Indices: 3734786--3734811 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3734776 CGATAACGAT
3734786 TCATAACTAAGA
1 TCATAACTAAGA
3734798 TCATAACTAAGA
1 TCATAACTAAGA
3734810 TC
1 TC
3734812 TTCAGTCAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (12 bp):
TCATAACTAAGA
Found at i:3741054 original size:14 final size:15
Alignment explanation
Indices: 3741019--3741055 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3741009 CACTCTCCTC
*
3741019 TTTGCTCCTCTTCGT
1 TTTGCTTCTCTTCGT
3741034 TTT-CTTCTCTT-GT
1 TTTGCTTCTCTTCGT
3741047 TTTGCTTCT
1 TTTGCTTCT
3741056 TTGAGCGACG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 12 0.60
15 3 0.15
ACGTcount: A:0.00, C:0.27, G:0.11, T:0.62
Consensus pattern (15 bp):
TTTGCTTCTCTTCGT
Found at i:3744462 original size:18 final size:18
Alignment explanation
Indices: 3744431--3744480 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
3744421 TTAATTTTAA
* * *
3744431 TAATGTTATCATTATTTT
1 TAATATTATTATTATGTT
*
3744449 TACTATTATTATTATGTT
1 TAATATTATTATTATGTT
*
3744467 TAATATTGTTATTA
1 TAATATTATTATTA
3744481 CTATTACCTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (18 bp):
TAATATTATTATTATGTT
Found at i:3751695 original size:29 final size:28
Alignment explanation
Indices: 3751649--3751709 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
3751639 GAATTCGCTA
3751649 TGTTTTTTTTTTCAGAGAAAATTGATAG
1 TGTTTTTTTTTTCAGAGAAAATTGATAG
** *
3751677 TGTTTTTTTTTTGTTGAGAAAATTGATGG
1 TGTTTTTTTTTT-CAGAGAAAATTGATAG
3751706 TGTT
1 TGTT
3751710 AAGGCAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 12 0.41
29 17 0.59
ACGTcount: A:0.23, C:0.02, G:0.21, T:0.54
Consensus pattern (28 bp):
TGTTTTTTTTTTCAGAGAAAATTGATAG
Found at i:3754481 original size:22 final size:23
Alignment explanation
Indices: 3754456--3754500 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
3754446 TCGTAATGAC
*
3754456 ATATGAAATTAACAATA-TAAAT
1 ATATCAAATTAACAATACTAAAT
*
3754478 ATATCAAATTAATAATACTAAAT
1 ATATCAAATTAACAATACTAAAT
3754501 GTATTACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
ATATCAAATTAACAATACTAAAT
Found at i:3758972 original size:29 final size:30
Alignment explanation
Indices: 3758913--3758970 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3758903 TCCGAGCCTT
*
3758913 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
3758943 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
3758971 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:3759199 original size:13 final size:13
Alignment explanation
Indices: 3759181--3759211 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3759171 TTCCAGCAAC
3759181 TATGAATTTATTT
1 TATGAATTTATTT
3759194 TATGAATTTATTT
1 TATGAATTTATTT
*
3759207 GATGA
1 TATGA
3759212 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:3759381 original size:50 final size:50
Alignment explanation
Indices: 3759306--3759548 Score: 387
Period size: 50 Copynumber: 4.8 Consensus size: 50
3759296 ATTTGGGTAA
3759306 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
3759356 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
3759406 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
3759456 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
3759506 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
3759549 TGTTATTATC
Statistics
Matches: 179, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
50 145 0.81
51 34 0.19
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:3768803 original size:2 final size:2
Alignment explanation
Indices: 3768796--3768832 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3768786 GGTTCTGATC
*
3768796 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3768833 TTAAGATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3770560 original size:17 final size:17
Alignment explanation
Indices: 3770538--3770573 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3770528 AAACAACTCT
3770538 AATTTAAGGCATCAATA
1 AATTTAAGGCATCAATA
*
3770555 AATTTAAGGCATCAGTA
1 AATTTAAGGCATCAATA
3770572 AA
1 AA
3770574 AAAGAAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (17 bp):
AATTTAAGGCATCAATA
Found at i:3772594 original size:5 final size:6
Alignment explanation
Indices: 3772577--3772601 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3772567 AAAAAGGTGA
3772577 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
3772602 TTGAAATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:3775617 original size:22 final size:22
Alignment explanation
Indices: 3775592--3775637 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
3775582 TATTGTCATC
* *
3775592 AACAATTTTGCACGTAAAGAAA
1 AACAATTTTACACGCAAAGAAA
*
3775614 AACAATTTTACATGCAAAGAAA
1 AACAATTTTACACGCAAAGAAA
3775636 AA
1 AA
3775638 TGAAAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.54, C:0.13, G:0.11, T:0.22
Consensus pattern (22 bp):
AACAATTTTACACGCAAAGAAA
Found at i:3776502 original size:28 final size:28
Alignment explanation
Indices: 3776459--3776536 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
3776449 TCTAAAAAAA
* * *
3776459 ATAAAAATTTACTAAAACTA-TAAAAACTG
1 ATAAAAAATTA-TAAAAATATTAAAAA-TC
*
3776488 ATAAAAAATTATAAAAATATTAGAAATC
1 ATAAAAAATTATAAAAATATTAAAAATC
*
3776516 ATAAAAGATTATAAAAA-ATTA
1 ATAAAAAATTATAAAAATATTA
3776537 TAAAGAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
27 4 0.09
28 24 0.56
29 15 0.35
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (28 bp):
ATAAAAAATTATAAAAATATTAAAAATC
Found at i:3776531 original size:10 final size:10
Alignment explanation
Indices: 3776472--3776550 Score: 63
Period size: 10 Copynumber: 8.1 Consensus size: 10
3776462 AAAATTTACT
*
3776472 AAAACTATAA
1 AAAATTATAA
* *
3776482 AAACTGATAA
1 AAAATTATAA
3776492 AAAATTAT-A
1 AAAATTATAA
*
3776501 AAAA-TATTA
1 AAAATTATAA
* *
3776510 GAAATCATAA
1 AAAATTATAA
*
3776520 AAGATTATAA
1 AAAATTATAA
3776530 AAAATTATAA
1 AAAATTATAA
* *
3776540 AGAATTTTAA
1 AAAATTATAA
3776550 A
1 A
3776551 CAATAGTAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
8 3 0.06
9 9 0.17
10 41 0.77
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (10 bp):
AAAATTATAA
Found at i:3776550 original size:20 final size:19
Alignment explanation
Indices: 3776489--3776564 Score: 66
Period size: 20 Copynumber: 3.9 Consensus size: 19
3776479 TAAAAACTGA
*
3776489 TAAAAAATTATAAAAATAT
1 TAAAAAATTATAAAAATTT
* * *
3776508 T-AGAAATCATAAAAGATTA
1 TAAAAAATTATAAAA-ATTT
3776527 TAAAAAATTATAAAGAATTT
1 TAAAAAATTATAAA-AATTT
*
3776547 TAAACAA-TAGTAAAAATT
1 TAAAAAATTA-TAAAAATT
3776565 GTTATATCTT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
18 11 0.24
19 10 0.22
20 23 0.51
21 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (19 bp):
TAAAAAATTATAAAAATTT
Found at i:3776892 original size:20 final size:20
Alignment explanation
Indices: 3776855--3776910 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
3776845 AGATAAATAT
3776855 TTATCTTGAGATAA-TAAAAAA
1 TTAT-TTGA-ATAATTAAAAAA
3776876 -TATTTTGAATAATTAAAAAA
1 TTA-TTTGAATAATTAAAAAA
*
3776896 TTATTTAAATAATTA
1 TTATTTGAATAATTA
3776911 TTTAATTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 4 0.13
20 24 0.77
21 3 0.10
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (20 bp):
TTATTTGAATAATTAAAAAA
Found at i:3777213 original size:36 final size:35
Alignment explanation
Indices: 3777173--3777253 Score: 94
Period size: 37 Copynumber: 2.3 Consensus size: 35
3777163 TTTTTTTTGT
3777173 AATTTTATAGTTTTAT-ATTTTTTTCTATTTTTAATA
1 AATTTTATA-TTTTATAATTTTTTTCTATTTTTAA-A
*
3777209 AATTTGTCAT-TTTTATAATTTTTTTTTATTTTTAAA
1 AATTT-T-ATATTTTATAATTTTTTTCTATTTTTAAA
*
3777245 AATTCTATA
1 AATTTTATA
3777254 AAGTTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
34 2 0.05
35 1 0.03
36 16 0.41
37 18 0.46
38 2 0.05
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (35 bp):
AATTTTATATTTTATAATTTTTTTCTATTTTTAAA
Found at i:3778335 original size:303 final size:303
Alignment explanation
Indices: 3777785--3778350 Score: 821
Period size: 303 Copynumber: 1.9 Consensus size: 303
3777775 GTTACATGCA
* * * *
3777785 ATTACTAGTCTTATACTATTCATGCAATTGTAGATTTATTCCATATTCTCCAATTGGATCATTCT
1 ATTACTAGTCTTACACTATTCATACAATTGTAGATTTACTCCATATTCTCCAATTAGATCATTCT
* * * * * * *
3777850 AAATCTTTGTACTTTTTGGATTTTGAAATTTCAGTATTAACGTAAAATGACTTTTGTTAATCCAT
66 AAATCTCTATACTTTTCGAATTTTAAAATTTCAATATTAACGTAAAATAACTTTTGTTAATCCAT
* *
3777915 TAATTAGATTTTAGTGAGTAATATATGAAAAATAATAATCTAACATGACATTACACATATAATAA
131 TAATGAGATTTTAATGAGTAATATATGAAAAATAATAATCTAACATGACATTACACATATAATAA
* * * * * **
3777980 AATGTTTGACGCATTAGATTTTAGAAATGGTAAAATTTTACTTAACGGTTTTAACAATTTATTAT
196 AATATATGACACATTAAATTTTAAAAATAATAAAATTTTACTTAACGGTTTTAACAATTTATTAT
3778045 TTGACGAATATTGAAAATTTAAAAAAAAAACTAAAAATGACCC
261 TTGACGAATATTGAAAATTTAAAAAAAAAACTAAAAATGACCC
* * * * *
3778088 ATTACTAGTCTTGCACTATTCATACAGTTGTAGATTTACTCTATATTCTCTATTTAGATCATTCT
1 ATTACTAGTCTTACACTATTCATACAATTGTAGATTTACTCCATATTCTCCAATTAGATCATTCT
* *
3778153 AAATCTCTATACTTTTCGAATTTTAAAATTTCAATCTTAACGTAAAATAATTTTTGTTAATCCAT
66 AAATCTCTATACTTTTCGAATTTTAAAATTTCAATATTAACGTAAAATAACTTTTGTTAATCCAT
* *
3778218 TAACTGA-ATTTTAATGAGTAATATGTAGAAAAA-AATAATCTAACATGACATTACATATATAAT
131 TAA-TGAGATTTTAATGAGTAATATAT-GAAAAATAATAATCTAACATGACATTACACATATAAT
* *
3778281 AAAATATATGACACATTAAATTTTAAAAATAATAAATTTTTACTTAATGGTTTTAACAATTTATT
194 AAAATATATGACACATTAAATTTTAAAAATAATAAAATTTTACTTAACGGTTTTAACAATTTATT
3778346 ATTTG
259 ATTTG
3778351 GTGAGAATTA
Statistics
Matches: 230, Mismatches: 31, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
303 222 0.97
304 8 0.03
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (303 bp):
ATTACTAGTCTTACACTATTCATACAATTGTAGATTTACTCCATATTCTCCAATTAGATCATTCT
AAATCTCTATACTTTTCGAATTTTAAAATTTCAATATTAACGTAAAATAACTTTTGTTAATCCAT
TAATGAGATTTTAATGAGTAATATATGAAAAATAATAATCTAACATGACATTACACATATAATAA
AATATATGACACATTAAATTTTAAAAATAATAAAATTTTACTTAACGGTTTTAACAATTTATTAT
TTGACGAATATTGAAAATTTAAAAAAAAAACTAAAAATGACCC
Found at i:3782333 original size:49 final size:48
Alignment explanation
Indices: 3782264--3782366 Score: 124
Period size: 46 Copynumber: 2.1 Consensus size: 48
3782254 ATATTTTAAA
3782264 ATTATTTTATGGTACAAATAAATTATAAAAATAAAC-TTAAATT-AAAATAT
1 ATTATTTTATGGTACAAATAAA--A-AAAAA-AAACATTAAATTCAAAATAT
* *
3782314 ATTATTTT-TTGTACAAATAAAAAATAAAAACATTAAATTCAAAATAT
1 ATTATTTTATGGTACAAATAAAAAAAAAAAACATTAAATTCAAAATAT
3782361 A-TATTT
1 ATTATTT
3782367 AAATTGATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
45 4 0.08
46 16 0.33
47 9 0.18
49 12 0.24
50 8 0.16
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (48 bp):
ATTATTTTATGGTACAAATAAAAAAAAAAAACATTAAATTCAAAATAT
Found at i:3782698 original size:39 final size:38
Alignment explanation
Indices: 3782614--3782699 Score: 95
Period size: 40 Copynumber: 2.3 Consensus size: 38
3782604 TTTATAATAT
* * *
3782614 ATTT-AAA-ATTATTTTTTGTACAGATAAATTATAAAA
1 ATTTAAAATATTAATTTTTGTACAAATAAATAATAAAA
**
3782650 ATAAAAAAATATTAATTTTTGTTACAAATAAATAATAAAA
1 AT-TTAAAATATTAATTTTTG-TACAAATAAATAATAAAA
3782690 ATTTAAAATA
1 ATTTAAAATA
3782700 CATTTTAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
36 2 0.05
38 3 0.08
39 16 0.41
40 18 0.46
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (38 bp):
ATTTAAAATATTAATTTTTGTACAAATAAATAATAAAA
Found at i:3788671 original size:44 final size:42
Alignment explanation
Indices: 3788589--3788671 Score: 96
Period size: 42 Copynumber: 1.9 Consensus size: 42
3788579 GCATTATGAG
* * **
3788589 TATAATATATAGTTTTTTATATTATTTATATTTTATAAAGGT
1 TATAATATATAGTTTATTATATTATTTATAATAAATAAAGGT
3788631 TATAATATATA-TTATATTATAATGTATTTATAATAAATAAA
1 TATAATATATAGTT-TATTAT-AT-TATTTATAATAAATAAA
3788672 AAAACAAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
41 2 0.06
42 16 0.47
43 2 0.06
44 14 0.41
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (42 bp):
TATAATATATAGTTTATTATATTATTTATAATAAATAAAGGT
Found at i:3790547 original size:42 final size:42
Alignment explanation
Indices: 3790457--3790549 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 42
3790447 GCTTAGCGCT
* *
3790457 TAGCAGACTTAATGCCGGTGAAACAATTTTAGACTTTATGTC
1 TAGCAGGCTTAATGCCGGTGAAACAATTTTAGACTATATGTC
3790499 TAGCAGGCTTAATGCCGGTGAAACAATTTTAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACAATTTTAGACTATATGTC
*
3790541 TCGCAGGCT
1 TAGCAGGCT
3790550 AAGTGTCAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (42 bp):
TAGCAGGCTTAATGCCGGTGAAACAATTTTAGACTATATGTC
Found at i:3793190 original size:21 final size:21
Alignment explanation
Indices: 3793164--3793216 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3793154 AACTGAGGCG
*
3793164 GTGAGATTAGTTACAGTAGCA
1 GTGAGATTAGATACAGTAGCA
* * *
3793185 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACAGTAGCA
3793206 GTGAGATTAGA
1 GTGAGATTAGA
3793217 AACAATGGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.08, G:0.34, T:0.28
Consensus pattern (21 bp):
GTGAGATTAGATACAGTAGCA
Found at i:3795146 original size:146 final size:146
Alignment explanation
Indices: 3794882--3795171 Score: 544
Period size: 146 Copynumber: 2.0 Consensus size: 146
3794872 TGACCTGCAT
*
3794882 AATTTGAATCCATACGCAGTTGCATAGTGAAATAAGTTTCATGGTGTACCAATACACTGCTCAAC
1 AATTTAAATCCATACGCAGTTGCATAGTGAAATAAGTTTCATGGTGTACCAATACACTGCTCAAC
* *
3794947 ACATATTCTTCCTCTTCATGATAATTGTTGTGCTCAACTTGGGTAACAATTGTGGCTATTCTTTG
66 ACATATTCTTCATCTTCATGATAATTGTTGTGCTCAACTTGGGTAACAATTGTGGCTATTCTTCG
3795012 TTGAGCTTCTTCACCC
131 TTGAGCTTCTTCACCC
3795028 AATTTAAATCCATACGCAGTTGCATAGTGAAATAAGTTTCATGGTGTACCAATACACTGCTCAAC
1 AATTTAAATCCATACGCAGTTGCATAGTGAAATAAGTTTCATGGTGTACCAATACACTGCTCAAC
*
3795093 ACATATTCTTTATCTTCATGATAATTGTTGTGCTCAACTTGGGTAACAATTGTGGCTATTCTTCG
66 ACATATTCTTCATCTTCATGATAATTGTTGTGCTCAACTTGGGTAACAATTGTGGCTATTCTTCG
3795158 TTGAGCTTCTTCAC
131 TTGAGCTTCTTCAC
3795172 TTAATTCAGG
Statistics
Matches: 140, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
146 140 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (146 bp):
AATTTAAATCCATACGCAGTTGCATAGTGAAATAAGTTTCATGGTGTACCAATACACTGCTCAAC
ACATATTCTTCATCTTCATGATAATTGTTGTGCTCAACTTGGGTAACAATTGTGGCTATTCTTCG
TTGAGCTTCTTCACCC
Found at i:3797473 original size:27 final size:27
Alignment explanation
Indices: 3797432--3797484 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
3797422 AACTGAGAAG
3797432 TGAATAGAAAACACAGAATATCTTATT
1 TGAATAGAAAACACAGAATATCTTATT
* * *
3797459 TGAATAGAAAGCACATAATATGTTAT
1 TGAATAGAAAACACAGAATATCTTAT
3797485 AGTTTCAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.30
Consensus pattern (27 bp):
TGAATAGAAAACACAGAATATCTTATT
Found at i:3801745 original size:29 final size:27
Alignment explanation
Indices: 3801707--3801765 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
3801697 TGGTATTAAT
3801707 AATTTCAAGATGTAATTGAAATATTTGAA
1 AATTTCAAGAT-TAATTGAAA-ATTTGAA
* * *
3801736 AATTTTAAGATTAATTTATAATTTGAA
1 AATTTCAAGATTAATTGAAAATTTGAA
3801763 AAT
1 AAT
3801766 ATTTTATTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 10 0.37
28 7 0.26
29 10 0.37
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (27 bp):
AATTTCAAGATTAATTGAAAATTTGAA
Found at i:3805552 original size:4 final size:4
Alignment explanation
Indices: 3805543--3805579 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
3805533 AAAAGAAGGT
3805543 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
3805580 GAGGGAGAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:3806448 original size:15 final size:15
Alignment explanation
Indices: 3806428--3806475 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 15
3806418 GTGAATTGGA
3806428 AATAAAAATATATTT
1 AATAAAAATATATTT
*
3806443 AATAAAAACTAATTTATT
1 AATAAAAA-T-ATAT-TT
3806461 AATAAAATATATATT
1 AATAAAA-ATATATT
3806476 AAAATGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 8 0.30
16 2 0.07
17 6 0.22
18 10 0.37
19 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAAAAATATATTT
Found at i:3806476 original size:15 final size:16
Alignment explanation
Indices: 3806428--3806477 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 16
3806418 GTGAATTGGA
3806428 AATAAAAATATAT-TT
1 AATAAAAATATATATT
*
3806443 AATAAAAACTAATTTATT
1 AATAAAAA-T-ATATATT
3806461 AAT-AAAATATATATT
1 AATAAAAATATATATT
3806476 AA
1 AA
3806478 AATGATTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 16 0.53
16 2 0.07
17 7 0.23
18 5 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
AATAAAAATATATATT
Found at i:3807004 original size:116 final size:117
Alignment explanation
Indices: 3806793--3807042 Score: 351
Period size: 116 Copynumber: 2.1 Consensus size: 117
3806783 CATCCAAACC
* * ** *
3806793 AACCTTGAGTCCGAAATTGAGAACTAGTAAGATGCATTCCTTCAACTATTGCTCTTCTAAACAGT
1 AACCCTGAGTCCAAAATTGAGAACTAGTAAGACACATTCCCTCAACTATTGCTCTTCTAAACAGT
* * *
3806858 TTCACTAGTGAAAATGCGGTGAGATAGAGAATAAATTGTATTGATGGCCTTA
66 CTCACTAGTGAAAATGCGGTGAGATAGAGAATAAATTGTACTGATGCCCTTA
* * * *
3806910 AATCCTGAGTCCAAAATTGAGAACTGGTGAGACACGTTCCCTCAACTGA-TGCTCTTC-AAACAG
1 AACCCTGAGTCCAAAATTGAGAACTAGTAAGACACATTCCCTCAACT-ATTGCTCTTCTAAACAG
* *
3806973 TCTCACTAGTGAAAATGCGGTGAGATGGAGAATAAATTGTACTGATGCCCTTT
65 TCTCACTAGTGAAAATGCGGTGAGATAGAGAATAAATTGTACTGATGCCCTTA
3807026 AACCCTGAGTCCAAAAT
1 AACCCTGAGTCCAAAAT
3807043 AAAAGTCAAC
Statistics
Matches: 117, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
116 70 0.60
117 46 0.39
118 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (117 bp):
AACCCTGAGTCCAAAATTGAGAACTAGTAAGACACATTCCCTCAACTATTGCTCTTCTAAACAGT
CTCACTAGTGAAAATGCGGTGAGATAGAGAATAAATTGTACTGATGCCCTTA
Found at i:3816768 original size:36 final size:39
Alignment explanation
Indices: 3816688--3816769 Score: 91
Period size: 36 Copynumber: 2.2 Consensus size: 39
3816678 TTTTTTATAA
*
3816688 ATTTT-TAAAAATTATTAGAATTTATATATTATTTATATG
1 ATTTTATAAAAATTATTAGAA-TTATATATTATTGATATG
* * *
3816727 TTTTTATAAAAATT-TTA-AA-TATATTTTATTGATTTG
1 ATTTTATAAAAATTATTAGAATTATATATTATTGATATG
3816763 ATTTTAT
1 ATTTTAT
3816770 TAGATTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
36 20 0.54
38 2 0.05
39 7 0.19
40 8 0.22
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (39 bp):
ATTTTATAAAAATTATTAGAATTATATATTATTGATATG
Found at i:3816789 original size:9 final size:9
Alignment explanation
Indices: 3816775--3816935 Score: 84
Period size: 9 Copynumber: 17.8 Consensus size: 9
3816765 TTTATTAGAT
3816775 TTTTTATAA
1 TTTTTATAA
3816784 TTTTTATAAA
1 TTTTTAT-AA
*
3816794 TTTTTAAATA
1 TTTTTATA-A
3816804 TATTTTATTAA
1 T-TTTTA-TAA
*
3816815 -TTTTATTA
1 TTTTTATAA
3816823 TTTTT-TAA
1 TTTTTATAA
*
3816831 --TATAT-A
1 TTTTTATAA
* *
3816837 TTTTTAGAT
1 TTTTTATAA
3816846 TTTTTATAA
1 TTTTTATAA
**
3816855 TACTTATAA
1 TTTTTATAA
* *
3816864 GTTATTATTA
1 -TTTTTATAA
*
3816874 TTGTTATAA
1 TTTTTATAA
3816883 TTTTTATAA
1 TTTTTATAA
*
3816892 GTTTATT-CAA
1 -TTT-TTATAA
*
3816902 TTTTAAT-A
1 TTTTTATAA
*
3816910 TATTTATAA
1 TTTTTATAA
3816919 TTTTTTATAA
1 -TTTTTATAA
3816929 TTTTTAT
1 TTTTTAT
3816936 GAGAAAATAT
Statistics
Matches: 113, Mismatches: 24, Indels: 30
0.68 0.14 0.18
Matches are distributed among these distances:
6 3 0.03
7 1 0.01
8 14 0.12
9 57 0.50
10 29 0.26
11 8 0.07
12 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:3816789 original size:21 final size:22
Alignment explanation
Indices: 3816763--3816823 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
3816753 TATTGATTTG
3816763 ATTTTATTAGATTTTTTATA-AT
1 ATTTTATTA-ATTTTTTATATAT
* *
3816785 -TTTTA-TAAATTTTTAAATAT
1 ATTTTATTAATTTTTTATATAT
3816805 ATTTTATTAATTTTATTAT
1 ATTTTATTAATTTT-TTAT
3816824 TTTTTAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
19 8 0.26
20 4 0.13
21 10 0.32
22 6 0.19
23 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTTATTAATTTTTTATATAT
Found at i:3816799 original size:19 final size:19
Alignment explanation
Indices: 3816775--3816935 Score: 72
Period size: 19 Copynumber: 8.8 Consensus size: 19
3816765 TTTATTAGAT
3816775 TTTTTATAATTTTTATAAA
1 TTTTTATAATTTTTATAAA
* *
3816794 TTTTTAAATATATTTTATTAA
1 TTTTTATA-AT-TTTTATAAA
*
3816815 -TTTTATTATTTTT-T-AA
1 TTTTTATAATTTTTATAAA
* * *
3816831 --TATAT-ATTTTTA-GAT
1 TTTTTATAATTTTTATAAA
** *
3816846 TTTTTATAATACTTATAAG
1 TTTTTATAATTTTTATAAA
* * *
3816865 TTATTATTATTGTTAT-AA
1 TTTTTATAATTTTTATAAA
* *
3816883 TTTTTATAA-GTTTATTCAA
1 TTTTTATAATTTTTA-TAAA
* * *
3816902 TTTTAAT-ATATTTATAAT
1 TTTTTATAATTTTTATAAA
3816920 TTTTTATAATTTTTAT
1 TTTTTATAATTTTTAT
3816936 GAGAAAATAT
Statistics
Matches: 104, Mismatches: 26, Indels: 24
0.68 0.17 0.16
Matches are distributed among these distances:
14 6 0.06
15 5 0.05
16 2 0.02
17 8 0.08
18 27 0.26
19 41 0.39
20 7 0.07
21 8 0.08
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTTATAATTTTTATAAA
Found at i:3816809 original size:67 final size:64
Alignment explanation
Indices: 3816699--3816825 Score: 141
Period size: 67 Copynumber: 1.9 Consensus size: 64
3816689 TTTTTAAAAA
**
3816699 TTATTAGAATTTATATATTATTTATATGTTTTTATAAAAATTTTAAATATATTTTATTGATTTGA
1 TTATTAGAATTTATATATTATTTATAAATTTTTATAAAAATTTT-AATA-ATTTTATT-ATTTGA
3816764 TT
63 TT
* * * *
3816766 TTATTAGATTTTTTATAATT-TTTATAAATTTTTA-AATATATTTTATTAATTTTATTATTT
1 TTATTAGAATTTATAT-ATTATTTATAAATTTTTATAA-AAATTTTAATAATTTTATTATTT
3816826 TTTAATATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
64 4 0.08
65 8 0.15
66 5 0.10
67 32 0.62
68 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (64 bp):
TTATTAGAATTTATATATTATTTATAAATTTTTATAAAAATTTTAATAATTTTATTATTTGATT
Found at i:3816835 original size:29 final size:29
Alignment explanation
Indices: 3816793--3816852 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
3816783 ATTTTTATAA
3816793 ATTTTTAAATATAT-TTTATTA-ATTTTATT
1 ATTTTTAAATATATATTT-TTAGATTTT-TT
*
3816822 ATTTTTTAATATATATTTTTAGATTTTTT
1 ATTTTTAAATATATATTTTTAGATTTTTT
3816851 AT
1 AT
3816853 AATACTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (29 bp):
ATTTTTAAATATATATTTTTAGATTTTTT
Found at i:3816838 original size:14 final size:14
Alignment explanation
Indices: 3816794--3816841 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
3816784 TTTTTATAAA
3816794 TTTTTAA-ATATAT
1 TTTTTAATATATAT
*
3816807 TTTATTAATTTTATTAT
1 TTT-TTAA-TATA-TAT
3816824 TTTTTAATATATAT
1 TTTTTAATATATAT
3816838 TTTT
1 TTTT
3816842 AGATTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 3 0.10
14 11 0.38
15 3 0.10
16 6 0.21
17 6 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTTAATATATAT
Found at i:3828425 original size:14 final size:14
Alignment explanation
Indices: 3828408--3828453 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
3828398 TAAAAAAATG
3828408 TTATTAAATTATTA
1 TTATTAAATTATTA
*
3828422 TTATTAAATTAGTA
1 TTATTAAATTATTA
3828436 TTATTAAATTATTA
1 TTATTAAATTATTA
3828450 TTAT
1 TTAT
3828454 ATTTTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TTATTAAATTATTA
Found at i:3829781 original size:23 final size:23
Alignment explanation
Indices: 3829754--3829864 Score: 142
Period size: 23 Copynumber: 5.0 Consensus size: 23
3829744 GGCTTTGCCG
* *
3829754 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACCTCATGTGTCGTAT
3829777 ATCAGGCACCTCATGTGTCGTAT
1 ATCAGGCACCTCATGTGTCGTAT
*
3829800 ATCAGGCACCTCGTGTGTCG--T
1 ATCAGGCACCTCATGTGTCGTAT
*
3829821 ATCAGGCACCTCGTGTGTCGT-T
1 ATCAGGCACCTCATGTGTCGTAT
*
3829843 -TCAGGCA-CTTATGTGTCGTAT
1 ATCAGGCACCTCATGTGTCGTAT
3829864 A
1 A
3829865 CTGATCAGGT
Statistics
Matches: 80, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
20 10 0.12
21 29 0.36
22 1 0.01
23 40 0.50
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.33
Consensus pattern (23 bp):
ATCAGGCACCTCATGTGTCGTAT
Found at i:3829839 original size:44 final size:41
Alignment explanation
Indices: 3829755--3829863 Score: 128
Period size: 44 Copynumber: 2.5 Consensus size: 41
3829745 GCTTTGCCGA
*
3829755 TCAGGCACTTTATGTGTCGTATATCAGGCACCTCATGTGTCGTAT
1 TCAGGCAC-TCATGTGTCG--TATCAGGCACCTCATGTGTCGT-T
* *
3829800 ATCAGGCACCTCGTGTGTCGTATCAGGCACCTCGTGTGTCGTT
1 -TCAGGCA-CTCATGTGTCGTATCAGGCACCTCATGTGTCGTT
*
3829843 TCAGGCACTTATGTGTCGTAT
1 TCAGGCACTCATGTGTCGTAT
3829864 ACTGATCAGG
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
41 12 0.21
42 7 0.12
43 1 0.02
44 21 0.37
46 15 0.26
47 1 0.02
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.34
Consensus pattern (41 bp):
TCAGGCACTCATGTGTCGTATCAGGCACCTCATGTGTCGTT
Found at i:3830541 original size:9 final size:9
Alignment explanation
Indices: 3830527--3830554 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3830517 GAATATGAAA
3830527 TGAATTGGT
1 TGAATTGGT
3830536 TGAATTGGT
1 TGAATTGGT
3830545 TGAATTGGT
1 TGAATTGGT
3830554 T
1 T
3830555 ATGTTTGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.46
Consensus pattern (9 bp):
TGAATTGGT
Found at i:3836708 original size:12 final size:12
Alignment explanation
Indices: 3836687--3836716 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3836677 AAATAAACTC
*
3836687 AAATATTAATTA
1 AAATAATAATTA
3836699 AAATAATAATTA
1 AAATAATAATTA
3836711 AAATAA
1 AAATAA
3836717 ATTATAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATAATAATTA
Found at i:3843174 original size:22 final size:22
Alignment explanation
Indices: 3843148--3843189 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3843138 TGCCAATCGA
3843148 AAGAG-AGAAAGAAGAAGAAAAG
1 AAGAGAAG-AAGAAGAAGAAAAG
*
3843170 AAGAGAAGAAGAAGGAGAAA
1 AAGAGAAGAAGAAGAAGAAA
3843190 GAGAGGGCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (22 bp):
AAGAGAAGAAGAAGAAGAAAAG
Found at i:3844960 original size:11 final size:11
Alignment explanation
Indices: 3844933--3844978 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
3844923 ATTAATCCTT
*
3844933 TCTCAATTATTC
1 TCTCAATT-TCC
3844945 TCTCAATTTCC
1 TCTCAATTTCC
*
3844956 TCTCAATTTGC
1 TCTCAATTTCC
*
3844967 TATCAATTTCC
1 TCTCAATTTCC
3844978 T
1 T
3844979 TCCAAATTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
11 22 0.73
12 8 0.27
ACGTcount: A:0.22, C:0.28, G:0.02, T:0.48
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:3844975 original size:22 final size:23
Alignment explanation
Indices: 3844933--3844978 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
3844923 ATTAATCCTT
* *
3844933 TCTCAATTATTCTCTCAATTTCC
1 TCTCAATTATGCTATCAATTTCC
3844956 TCTCAATT-TGCTATCAATTTCC
1 TCTCAATTATGCTATCAATTTCC
3844978 T
1 T
3844979 TCCAAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.22, C:0.28, G:0.02, T:0.48
Consensus pattern (23 bp):
TCTCAATTATGCTATCAATTTCC
Found at i:3844994 original size:22 final size:21
Alignment explanation
Indices: 3844933--3844994 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 21
3844923 ATTAATCCTT
3844933 TCTCAATTATTCTCTCAATTTCC
1 TCTCAA-T-TTCTCTCAATTTCC
*
3844956 TCTCAATTTGCTATCAATTTCC
1 TCTCAATTT-CTCTCAATTTCC
3844978 T-TCCAAATTTCTCTCAA
1 TCT-C-AATTTCTCTCAA
3844995 ATCCATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 3 0.09
22 20 0.59
23 11 0.32
ACGTcount: A:0.24, C:0.29, G:0.02, T:0.45
Consensus pattern (21 bp):
TCTCAATTTCTCTCAATTTCC
Found at i:3846629 original size:63 final size:63
Alignment explanation
Indices: 3846553--3846677 Score: 241
Period size: 63 Copynumber: 2.0 Consensus size: 63
3846543 TCGTTCTGGA
*
3846553 GTTAGCGTGCGTGCTGGAAGACATGCCATAGTTTAGGATCCATGACAAGCCGTATTTACTGTT
1 GTTAGCGTGCGTGCTAGAAGACATGCCATAGTTTAGGATCCATGACAAGCCGTATTTACTGTT
3846616 GTTAGCGTGCGTGCTAGAAGACATGCCATAGTTTAGGATCCATGACAAGCCGTATTTACTGT
1 GTTAGCGTGCGTGCTAGAAGACATGCCATAGTTTAGGATCCATGACAAGCCGTATTTACTGT
3846678 CGGCAAAGGA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (63 bp):
GTTAGCGTGCGTGCTAGAAGACATGCCATAGTTTAGGATCCATGACAAGCCGTATTTACTGTT
Found at i:3846952 original size:18 final size:18
Alignment explanation
Indices: 3846911--3846945 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3846901 GCCAGGTGCG
*
3846911 TATCCTAACCCTTTTATA
1 TATCCTAACCCTTATATA
3846929 TATCCTAACCCTTATAT
1 TATCCTAACCCTTATAT
3846946 GTTTCCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (18 bp):
TATCCTAACCCTTATATA
Found at i:3847233 original size:21 final size:21
Alignment explanation
Indices: 3847207--3847255 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3847197 TAGATACCCT
* *
3847207 ACCGGAAAAACCATAATCCCC
1 ACCGGAAAAACCACAACCCCC
*
3847228 ACCGGATAAACCACAACCCCC
1 ACCGGAAAAACCACAACCCCC
*
3847249 TCCGGAA
1 ACCGGAA
3847256 GCTGGACAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.41, G:0.12, T:0.08
Consensus pattern (21 bp):
ACCGGAAAAACCACAACCCCC
Found at i:3851173 original size:26 final size:27
Alignment explanation
Indices: 3851132--3851196 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 27
3851122 TATAATAAAT
3851132 AAATA-TTTTTTATTC-TTTAATTTTA
1 AAATATTTTTTTATTCTTTTAATTTTA
*
3851157 AAATATTTTTTTATTCTTTTTATTTTTA
1 AAATATTTTTTTATTC-TTTTAATTTTA
3851185 AAATATTTTTTT
1 AAATATTTTTTT
3851197 TGGTGTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
25 5 0.14
26 10 0.28
28 21 0.58
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (27 bp):
AAATATTTTTTTATTCTTTTAATTTTA
Found at i:3851205 original size:27 final size:28
Alignment explanation
Indices: 3851132--3851207 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 28
3851122 TATAATAAAT
* *
3851132 AAATA-TTTTTTAT--TCTTTAATTTTA
1 AAATATTTTTTTATGCTGTTTATTTTTA
* *
3851157 AAATATTTTTTTATTCTTTTTATTTTTA
1 AAATATTTTTTTATGCTGTTTATTTTTA
*
3851185 AAATATTTTTTT-TGGTGTTTATT
1 AAATATTTTTTTATGCTGTTTATT
3851208 AAAAATGGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
25 5 0.12
26 8 0.19
27 8 0.19
28 22 0.51
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.67
Consensus pattern (28 bp):
AAATATTTTTTTATGCTGTTTATTTTTA
Found at i:3851532 original size:40 final size:38
Alignment explanation
Indices: 3851465--3851578 Score: 110
Period size: 40 Copynumber: 2.9 Consensus size: 38
3851455 GCAATGAATC
* *
3851465 AGGCAAAACGCGTCCCTGAGGGA-GCGTTTTGCCTACGT
1 AGGCAAAACGC-TCCCTTAAGGACGCGTTTTGCCTACGT
3851503 -GGACATAAAGCGCTCCCTTAAGGACGCGTTTTATGTCC-ACGT
1 AGG-CA-AAA-CGCTCCCTTAAGGACGCG-TTT-TG-CCTACGT
*
3851545 AGGCAAAACGCTCCCTTATGGACGCGTTTT-CCTA
1 AGGCAAAACGCTCCCTTAAGGACGCGTTTTGCCTA
3851579 TCACGTACCC
Statistics
Matches: 64, Mismatches: 3, Indels: 19
0.74 0.03 0.22
Matches are distributed among these distances:
36 2 0.03
37 3 0.05
38 3 0.05
39 15 0.23
40 23 0.36
41 6 0.09
42 8 0.12
43 4 0.06
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (38 bp):
AGGCAAAACGCTCCCTTAAGGACGCGTTTTGCCTACGT
Found at i:3852967 original size:14 final size:14
Alignment explanation
Indices: 3852948--3852982 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
3852938 ACATTTTTTT
*
3852948 TTCTAATGATACTA
1 TTCTAACGATACTA
3852962 TTCTAACGATACTA
1 TTCTAACGATACTA
3852976 TTCTAAC
1 TTCTAAC
3852983 ATGTAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:3854317 original size:16 final size:15
Alignment explanation
Indices: 3854296--3854326 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
3854286 TAGAATCGGG
3854296 AGTCGCCGAGTCACCA
1 AGTCGCCGAGT-ACCA
3854312 AGTCGCCGAGTACCA
1 AGTCGCCGAGTACCA
3854327 GGTTTGCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.26, C:0.35, G:0.26, T:0.13
Consensus pattern (15 bp):
AGTCGCCGAGTACCA
Found at i:3858007 original size:24 final size:24
Alignment explanation
Indices: 3857950--3858008 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
3857940 GGTTTAATGC
* *
3857950 AAATGGAGATATTTTGGAGAGATG
1 AAATGGATATATTTTGGAAAGATG
*
3857974 AAATGAATATATTTTGGAAAGATG
1 AAATGGATATATTTTGGAAAGATG
3857998 AAATGGATATA
1 AAATGGATATA
3858009 AATGGAGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (24 bp):
AAATGGATATATTTTGGAAAGATG
Found at i:3858100 original size:20 final size:19
Alignment explanation
Indices: 3858074--3858138 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
3858064 AATATTTTTA
3858074 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
* ***
3858093 ACTTATGTAAT-ATTTTTA-
1 A-TTATGTAGTGATTCAAAG
3858111 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
3858130 ATTTATGTA
1 A-TTATGTA
3858139 ATGTTTTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
17 8 0.24
18 5 0.15
19 6 0.18
20 15 0.44
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (19 bp):
ATTATGTAGTGATTCAAAG
Found at i:3858103 original size:37 final size:37
Alignment explanation
Indices: 3858049--3858161 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
3858039 TTATGTTTTA
*
3858049 ATTC-AAGACTTGTGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
3858085 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
* *
3858122 ATTCAAAGATTTATGTAATGTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
3858159 ATT
1 ATT
3858162 TAATTCGGGT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 4 0.05
37 69 0.95
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (37 bp):
ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
Found at i:3858117 original size:17 final size:17
Alignment explanation
Indices: 3858061--3858155 Score: 55
Period size: 17 Copynumber: 5.2 Consensus size: 17
3858051 TCAAGACTTG
3858061 TGTAATATTTTTAATTA
1 TGTAATATTTTTAATTA
* ***
3858078 TGTAGTGATTCAAAGACTTA
1 TGTAAT-ATTTTTA-A-TTA
3858098 TGTAATATTTTTAATTA
1 TGTAATATTTTTAATTA
* ***
3858115 TGTAGTGATTCAAAGATTTA
1 TGTAAT-ATTTTTA-A-TTA
*
3858135 TGTAATGTTTTTAATTA
1 TGTAATATTTTTAATTA
3858152 TGTA
1 TGTA
3858156 GTGATTTAAT
Statistics
Matches: 55, Mismatches: 17, Indels: 12
0.65 0.20 0.14
Matches are distributed among these distances:
17 20 0.36
18 10 0.18
19 9 0.16
20 16 0.29
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (17 bp):
TGTAATATTTTTAATTA
Found at i:3858176 original size:9 final size:9
Alignment explanation
Indices: 3858162--3858280 Score: 157
Period size: 9 Copynumber: 12.6 Consensus size: 9
3858152 TGTAGTGATT
3858162 TAATTCGGG
1 TAATTCGGG
3858171 TAATTCGGG
1 TAATTCGGG
3858180 TAATTTTCGGG
1 TAA--TTCGGG
3858191 TAATTTTCGGG
1 TAA--TTCGGG
*
3858202 TAATTTGGG
1 TAATTCGGG
3858211 TAATTTTCGGG
1 TAA--TTCGGG
3858222 TAATTCGGG
1 TAATTCGGG
3858231 TAATTCGGG
1 TAATTCGGG
*
3858240 TAAGTCGGG
1 TAATTCGGG
3858249 TAATTCGGG
1 TAATTCGGG
*
3858258 TAAGTCGGG
1 TAATTCGGG
3858267 TAATTCGGG
1 TAATTCGGG
3858276 TAATT
1 TAATT
3858281 TTTAACCAAA
Statistics
Matches: 100, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
9 72 0.72
11 28 0.28
ACGTcount: A:0.22, C:0.09, G:0.32, T:0.37
Consensus pattern (9 bp):
TAATTCGGG
Found at i:3858418 original size:28 final size:27
Alignment explanation
Indices: 3858386--3858451 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
3858376 AAAATTCGGT
3858386 TCGGTTAACGGTTA-AAAAATTTGAGAGG
1 TCGGTTAACGGTTACAAAAATTT-AG-GG
* *
3858414 TCGGTTAATTCGGTTACAAGAATTTCGGG
1 TCGGTTAA--CGGTTACAAAAATTTAGGG
3858443 TCGGTTAAC
1 TCGGTTAAC
3858452 CGACTGAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
27 1 0.03
28 8 0.24
29 10 0.30
30 7 0.21
31 7 0.21
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (27 bp):
TCGGTTAACGGTTACAAAAATTTAGGG
Found at i:3858787 original size:48 final size:49
Alignment explanation
Indices: 3858670--3858788 Score: 195
Period size: 49 Copynumber: 2.4 Consensus size: 49
3858660 TTATTTATTT
* **
3858670 AATTAGATTAATTGCAACATTAAAACTTGGAATAAACTTTGTGGTCATA
1 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTAATCATA
*
3858719 AATTAGATTAATTGCAACATTGAAACTTGGAACAAACTTTGTAAT-ATA
1 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTAATCATA
3858767 AATTAGATTAATTGCAACATTA
1 AATTAGATTAATTGCAACATTA
3858789 CAATATTACA
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
48 24 0.37
49 41 0.63
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (49 bp):
AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTAATCATA
Found at i:3858809 original size:64 final size:63
Alignment explanation
Indices: 3858716--3858898 Score: 196
Period size: 64 Copynumber: 2.9 Consensus size: 63
3858706 CTTTGTGGTC
* * *
3858716 ATAAATTAGATTAATTGCAACATTGAAACTTGGAACAAACTTTGTAATATAAATTAGAT-TAAT
1 ATAAATTA-AATAATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAGATGTAAT
* *
3858779 -TGCAACATTACAAT-ATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAGTT--TTGTA
1 AT--AA-ATTA-AATAATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAGATGTA
3858840 AT
62 AT
* * **
3858842 ATAAATTAAATACATTACAATATTAAAAATCAGAACAAACTTTGTAATATAAATTAG
1 ATAAATTAAATA-ATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAG
3858899 GTACATTGGA
Statistics
Matches: 100, Mismatches: 11, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
60 3 0.03
61 4 0.04
62 41 0.41
63 4 0.04
64 42 0.42
65 6 0.06
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.34
Consensus pattern (63 bp):
ATAAATTAAATAATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAGATGTAAT
Found at i:3866878 original size:29 final size:30
Alignment explanation
Indices: 3866819--3866876 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3866809 TCCGAGCCTT
*
3866819 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* * *
3866849 GGGGTAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
3866877 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:3867106 original size:13 final size:13
Alignment explanation
Indices: 3867088--3867119 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3867078 TTTCCAGCAA
3867088 TTATGAATTTATT
1 TTATGAATTTATT
3867101 TTATGAATTTATT
1 TTATGAATTTATT
*
3867114 TGATGA
1 TTATGA
3867120 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:3867327 original size:50 final size:50
Alignment explanation
Indices: 3867214--3867455 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
3867204 ATTTGGGTAA
* * *
3867214 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
3867270 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
3867320 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
3867370 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
3867420 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
3867456 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:3867403 original size:100 final size:103
Alignment explanation
Indices: 3867214--3867463 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
3867204 ATTTGGGTAA
3867214 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
3867279 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
3867320 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
3867382 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
3867420 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
3867464 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:3869300 original size:18 final size:18
Alignment explanation
Indices: 3869265--3869299 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3869255 GGAAAAACCA
*
3869265 ATTTATCTTTTTATTTTT
1 ATTTATCTTTTGATTTTT
3869283 ATTTAT-TTTTGATTTTT
1 ATTTATCTTTTGATTTTT
3869300 TTAAGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (18 bp):
ATTTATCTTTTGATTTTT
Found at i:3870560 original size:21 final size:20
Alignment explanation
Indices: 3870527--3870574 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
3870517 CAAAATAAAG
3870527 AGGGCCACCCTC-TCTTGCCA
1 AGGGCCACCCTCTTC-TGCCA
*
3870547 AGGGACCACTCTCTTCTGCCA
1 AGGG-CCACCCTCTTCTGCCA
*
3870568 AAGGCCA
1 AGGGCCA
3870575 TTTTCACCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 7 0.29
21 15 0.62
22 2 0.08
ACGTcount: A:0.21, C:0.40, G:0.21, T:0.19
Consensus pattern (20 bp):
AGGGCCACCCTCTTCTGCCA
Found at i:3870594 original size:21 final size:21
Alignment explanation
Indices: 3870570--3870609 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3870560 TTCTGCCAAA
*
3870570 GGCCATTTTCACCCACCAATG
1 GGCCATTCTCACCCACCAATG
* *
3870591 GGCCGTTCTCACTCACCAA
1 GGCCATTCTCACCCACCAA
3870610 AGGGGTGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.40, G:0.15, T:0.23
Consensus pattern (21 bp):
GGCCATTCTCACCCACCAATG
Found at i:3871983 original size:33 final size:32
Alignment explanation
Indices: 3871946--3872022 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 32
3871936 TGGCCCTGCC
** * *
3871946 ATGGTCTTACATTTGTAGTGCCATAGCCCAGTT
1 ATGGTCTTACATCAG-AATGCCATAGCCCAGCT
3871979 ATGGTCTTATCATCAGAATGCCATAGCCCAGCT
1 ATGGTCTTA-CATCAGAATGCCATAGCCCAGCT
3872012 ATGGTCTTACA
1 ATGGTCTTACA
3872023 CATGTATCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
32 2 0.05
33 33 0.85
34 4 0.10
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.32
Consensus pattern (32 bp):
ATGGTCTTACATCAGAATGCCATAGCCCAGCT
Found at i:3872107 original size:105 final size:105
Alignment explanation
Indices: 3871967--3872232 Score: 383
Period size: 105 Copynumber: 2.5 Consensus size: 105
3871957 TTTGTAGTGC
* * * * *
3871967 CATAGCCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACACATGTATCT
1 CATAACCCAGTTATGGTCTTTTTATTAAAATGCCATAGCCCAGCTATGGTCTTACACATGTATCT
** * * *
3872032 ATACTGTTATGGTCCAACCAT-AGTCTTACGTTCAATG-TGT
66 ATACTGCCATGGTCCAACCATGA-TATTAAGTTCAA-GATAT
* *
3872072 CATAACCCAGTTATGATCTTTTTATTAAAATGCCATAGCTCAGCTATGGTCTTACACATGTATCT
1 CATAACCCAGTTATGGTCTTTTTATTAAAATGCCATAGCCCAGCTATGGTCTTACACATGTATCT
*
3872137 ATACTGCCATGGTCTAACCATGATATTAAGTTCAAGATAT
66 ATACTGCCATGGTCCAACCATGATATTAAGTTCAAGATAT
3872177 CATAACCCAGTTATGGTCTTTTTATTAAAATGCCATAGCCCAGCTATGGTCTTACA
1 CATAACCCAGTTATGGTCTTTTTATTAAAATGCCATAGCCCAGCTATGGTCTTACA
3872233 TTTAAACATT
Statistics
Matches: 144, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
104 1 0.01
105 142 0.99
106 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (105 bp):
CATAACCCAGTTATGGTCTTTTTATTAAAATGCCATAGCCCAGCTATGGTCTTACACATGTATCT
ATACTGCCATGGTCCAACCATGATATTAAGTTCAAGATAT
Found at i:3879128 original size:15 final size:16
Alignment explanation
Indices: 3879096--3879128 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3879086 GACTTGCTTG
3879096 AACTTGAAATCGAAAT
1 AACTTGAAATCGAAAT
*
3879112 AACTTGAATTC-AAAT
1 AACTTGAAATCGAAAT
3879127 AA
1 AA
3879129 GATTGAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.27
Consensus pattern (16 bp):
AACTTGAAATCGAAAT
Found at i:3879190 original size:15 final size:15
Alignment explanation
Indices: 3879165--3879209 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
3879155 GAAAATATTT
3879165 AAACTCAAAAAAATCC
1 AAACTC-AAAAAATCC
* *
3879181 TAACTCAAAAAACCC
1 AAACTCAAAAAATCC
*
3879196 AAATTCAAAAAATC
1 AAACTCAAAAAATC
3879210 TTAAACTTGA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (15 bp):
AAACTCAAAAAATCC
Found at i:3879564 original size:19 final size:19
Alignment explanation
Indices: 3879540--3879608 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 19
3879530 AAAAAGGAAC
3879540 TAAATAAAATATATTATAT
1 TAAATAAAATATATTATAT
* *
3879559 TAAAT--AATATA-AATTT
1 TAAATAAAATATATTATAT
*
3879575 TAAATAAAAT-TAATTATAA
1 TAAATAAAATAT-ATTATAT
*
3879594 T-AATTAAATATATTA
1 TAAATAAAATATATTA
3879609 CACATGACTG
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
16 8 0.21
17 7 0.18
18 15 0.38
19 9 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAATAAAATATATTATAT
Found at i:3882227 original size:22 final size:21
Alignment explanation
Indices: 3882169--3882238 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
3882159 AAATAATAGT
* * *
3882169 AAAATAGCGAGAAAACAATAAG
1 AAAATAG-TAGAAAACAGTAAA
*
3882191 AAAATAATAGCAAAACAGTAAA
1 AAAATAGTAG-AAAACAGTAAA
* *
3882213 AAAATAGTAAGAAAATAGCAAA
1 AAAATAGT-AGAAAACAGTAAA
3882235 AAAA
1 AAAA
3882239 AATAGCAGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 2 0.05
22 35 0.90
23 2 0.05
ACGTcount: A:0.69, C:0.07, G:0.13, T:0.11
Consensus pattern (21 bp):
AAAATAGTAGAAAACAGTAAA
Found at i:3883168 original size:22 final size:23
Alignment explanation
Indices: 3883143--3883188 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
3883133 ATATTTGTTC
* *
3883143 AAATGTATTATAATT-TAAATTT
1 AAATATATTACAATTATAAATTT
*
3883165 AAATATATTACAATTATCAATTT
1 AAATATATTACAATTATAAATTT
3883188 A
1 A
3883189 TTTATCATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATATATTACAATTATAAATTT
Found at i:3899901 original size:6 final size:6
Alignment explanation
Indices: 3899892--3899916 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3899882 TTTATTTTCT
3899892 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
3899917 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:3903111 original size:21 final size:19
Alignment explanation
Indices: 3903068--3903113 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3903058 AAATAAAAAT
*
3903068 AAAAATATAAAAAATTTAG
1 AAAAATATAAAAAATCTAG
* *
3903087 AAATATATATAAAATCTAG
1 AAAAATATAAAAAATCTAG
3903106 AAAAATAT
1 AAAAATAT
3903114 TTTTTTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (19 bp):
AAAAATATAAAAAATCTAG
Found at i:3903226 original size:20 final size:20
Alignment explanation
Indices: 3903186--3903245 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
3903176 TTTTTTCACG
*
3903186 ATTTTTA-TTTTT-ATATATT
1 ATTTTTATTTTTTAAAAT-TT
3903205 ATTTTTATTTTTTAAAATTT
1 ATTTTTATTTTTTAAAATTT
** * *
3903225 ATAATTATATATTAAAATTT
1 ATTTTTATTTTTTAAAATTT
3903245 A
1 A
3903246 GCATAAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 7 0.21
20 24 0.71
21 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTTTATTTTTTAAAATTT
Found at i:3903383 original size:25 final size:23
Alignment explanation
Indices: 3903353--3903404 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
3903343 TAAATTCTTA
*
3903353 TATTTTAATTTAAATTTAATATTTT
1 TATTTTAA-ATAAATTT-ATATTTT
*
3903378 TATTTTAAATAAATTTCTATTTT
1 TATTTTAAATAAATTTATATTTT
3903401 TATT
1 TATT
3903405 GGCCAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.40
24 7 0.28
25 8 0.32
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTTTAAATAAATTTATATTTT
Found at i:3910535 original size:24 final size:24
Alignment explanation
Indices: 3910507--3910554 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
3910497 AAAGTTACTC
3910507 TTTATACTTTTATTAAACTAATAA
1 TTTATACTTTTATTAAACTAATAA
*
3910531 TTTATACTTTTATTAAATTAATAA
1 TTTATACTTTTATTAAACTAATAA
3910555 GCTAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTATACTTTTATTAAACTAATAA
Found at i:3910802 original size:21 final size:20
Alignment explanation
Indices: 3910763--3910802 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3910753 ATTTTATTTT
*
3910763 TTTATTTTTAACTATTTAAA
1 TTTATTTTTAACTAATTAAA
*
3910783 TTTATATTTTAATTAATTAA
1 TTTAT-TTTTAACTAATTAA
3910803 TTAATTGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATTTTTAACTAATTAAA
Found at i:3910828 original size:16 final size:16
Alignment explanation
Indices: 3910807--3910844 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3910797 AATTAATTAA
3910807 TTGAG-TTATTTTATAT
1 TTGAGTTTA-TTTATAT
3910823 TTGAGTTTATTTATAT
1 TTGAGTTTATTTATAT
*
3910839 ATGAGT
1 TTGAGT
3910845 AATTGAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (16 bp):
TTGAGTTTATTTATAT
Found at i:3911385 original size:19 final size:18
Alignment explanation
Indices: 3911358--3911409 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
3911348 ATTTATAGGA
*
3911358 TTTTCAGTTTTTTTATAT
1 TTTTTAGTTTTTTTATAT
*
3911376 TTTTTAAGTTTATTATATAT
1 TTTTT-AGTTT-TTTTATAT
*
3911396 TCTTTAGTTTTTTT
1 TTTTTAGTTTTTTT
3911410 TATAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.25
19 10 0.36
20 11 0.39
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTTTAGTTTTTTTATAT
Found at i:3913334 original size:14 final size:15
Alignment explanation
Indices: 3913296--3913335 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
3913286 ACAATTTTAT
3913296 AACTTAAA--TTCAG
1 AACTTAAATTTTCAG
3913309 AACTTAAATTTTCAG
1 AACTTAAATTTTCAG
3913324 AACTT-AATTTTC
1 AACTTAAATTTTC
3913336 TGCATGGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.32
14 7 0.28
15 10 0.40
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (15 bp):
AACTTAAATTTTCAG
Found at i:3913461 original size:16 final size:16
Alignment explanation
Indices: 3913435--3913487 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
3913425 GAGCTTTGTT
*
3913435 TAATGGATTAGAGGTG
1 TAATAGATTAGAGGTG
*
3913451 TATTAGATTAGAGGTG
1 TAATAGATTAGAGGTG
* *
3913467 TAATGGAATAGAGGTG
1 TAATAGATTAGAGGTG
3913483 TAATA
1 TAATA
3913488 TCAAATCAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (16 bp):
TAATAGATTAGAGGTG
Found at i:3913747 original size:14 final size:15
Alignment explanation
Indices: 3913708--3913749 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3913698 TTTTAACATA
*
3913708 ATTATTATTAAATAT
1 ATTATAATTAAATAT
3913723 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
3913737 A-TATAATTTAATA
1 ATTATAATTAAATA
3913750 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:3917706 original size:20 final size:21
Alignment explanation
Indices: 3917681--3917731 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
3917671 TAGGAAAATT
*
3917681 TTATAAAAATATATT-ATATA
1 TTATAAAAATATATTAATAGA
*
3917701 TTATAAAAATTTATTAATAGA
1 TTATAAAAATATATTAATAGA
3917722 TTATAAAAAT
1 TTATAAAAAT
3917732 GTGGAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTATAAAAATATATTAATAGA
Found at i:3917936 original size:21 final size:21
Alignment explanation
Indices: 3917910--3917950 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3917900 TGGTGTGATA
*
3917910 GTTGACATGGCATTTCACATT
1 GTTGACATGACATTTCACATT
*
3917931 GTTGACATGACATTTGACAT
1 GTTGACATGACATTTCACAT
3917951 CAAAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (21 bp):
GTTGACATGACATTTCACATT
Found at i:3918129 original size:20 final size:21
Alignment explanation
Indices: 3918104--3918154 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
3918094 TAGGAAAATT
*
3918104 TTATAAAAATATATT-ATATA
1 TTATAAAAATATATTAATAGA
*
3918124 TTATAAAAATTTATTAATAGA
1 TTATAAAAATATATTAATAGA
3918145 TTATAAAAAT
1 TTATAAAAAT
3918155 GTGGAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTATAAAAATATATTAATAGA
Found at i:3918266 original size:27 final size:26
Alignment explanation
Indices: 3918236--3918295 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
3918226 GTAAATTATG
3918236 AAAAATATGAAATAATTA-TAAAAATCT
1 AAAAATAT-AAAT-ATTATTAAAAATCT
* *
3918263 AAAATAAATAAATATTATTAAAAATTT
1 AAAA-ATATAAATATTATTAAAAATCT
3918290 AAAAAT
1 AAAAAT
3918296 TGATGCGGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 5 0.18
27 20 0.71
28 3 0.11
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (26 bp):
AAAAATATAAATATTATTAAAAATCT
Found at i:3918267 original size:19 final size:20
Alignment explanation
Indices: 3918229--3918269 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
3918219 ATTATTAGTA
*
3918229 AATTATGAAAAATATGAAAT
1 AATTATGAAAAATATAAAAT
*
3918249 AATTAT-AAAAATCTAAAAT
1 AATTATGAAAAATATAAAAT
3918268 AA
1 AA
3918270 ATAAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (20 bp):
AATTATGAAAAATATAAAAT
Found at i:3925369 original size:45 final size:44
Alignment explanation
Indices: 3925285--3925375 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
3925275 TATAAAGTAT
* ** * *
3925285 TATCTAAATATTAATTTAGTAAAAATAAAGTTTAATAATTGTAA
1 TATCTAAATATTAATTAAGTAAAAATAAACATAAATAATTATAA
3925329 TATCTAAATATTAATTAAGTAAAAAATAAACATAAATAATTATAA
1 TATCTAAATATTAATTAAGT-AAAAATAAACATAAATAATTATAA
3925374 TA
1 TA
3925376 CTTAAAACAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 19 0.46
45 22 0.54
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.37
Consensus pattern (44 bp):
TATCTAAATATTAATTAAGTAAAAATAAACATAAATAATTATAA
Found at i:3928427 original size:16 final size:16
Alignment explanation
Indices: 3928390--3928428 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
3928380 TTTACTTTAT
3928390 GTAATTAATACAAAATA
1 GTAATT-ATACAAAATA
*
3928407 G-AATTATTCAAAATA
1 GTAATTATACAAAATA
3928422 GTAATTA
1 GTAATTA
3928429 AGAAATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 10 0.50
16 9 0.45
17 1 0.05
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (16 bp):
GTAATTATACAAAATA
Found at i:3937668 original size:21 final size:21
Alignment explanation
Indices: 3937644--3937683 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3937634 CAAAACGATG
3937644 TGGTTTT-ACTTTTTAACTTAA
1 TGGTTTTAAC-TTTTAACTTAA
3937665 TGGTTTTAACTTTTAACTT
1 TGGTTTTAACTTTTAACTT
3937684 TAGAAAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.57
Consensus pattern (21 bp):
TGGTTTTAACTTTTAACTTAA
Found at i:3943656 original size:39 final size:39
Alignment explanation
Indices: 3943602--3943687 Score: 118
Period size: 39 Copynumber: 2.2 Consensus size: 39
3943592 CAAAGAGAAT
* * * *
3943602 CATTGTTCGGTTATAAAGGTGTCAACAATAGACTTTAAC
1 CATTGCTCGATTATAAAGATGTCAACAAGAGACTTTAAC
*
3943641 CATTGCTCGATTATAAAGATGTCCACAAGAGACTTTAAC
1 CATTGCTCGATTATAAAGATGTCAACAAGAGACTTTAAC
*
3943680 TATTGCTC
1 CATTGCTC
3943688 CCTAATACTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (39 bp):
CATTGCTCGATTATAAAGATGTCAACAAGAGACTTTAAC
Found at i:3949895 original size:5 final size:5
Alignment explanation
Indices: 3949885--3949935 Score: 59
Period size: 5 Copynumber: 10.2 Consensus size: 5
3949875 GTTATAAATT
* * *
3949885 ATATA ATATA ATAT- ATATAA AAATA ACATA ATATA ATATA ATATA TTATA
1 ATATA ATATA ATATA ATAT-A ATATA ATATA ATATA ATATA ATATA ATATA
3949935 A
1 A
3949936 ATTTAAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
4 4 0.10
5 32 0.82
6 3 0.08
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:3958376 original size:23 final size:24
Alignment explanation
Indices: 3958329--3958376 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
3958319 GGTCAAAATT
* *
3958329 AAATCATAATTTTTATAATAGTAA
1 AAATCATAATTTTTAAAAGAGTAA
*
3958353 AAAT-ATAATTTTTAAAAGATTAA
1 AAATCATAATTTTTAAAAGAGTAA
3958376 A
1 A
3958377 TCAAAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATCATAATTTTTAAAAGAGTAA
Found at i:3960965 original size:6 final size:6
Alignment explanation
Indices: 3960956--3960988 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
3960946 TTTATTTTAT
3960956 TTAATA TTAATA TTAATA TTAATA TTAAT- TTAA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAA
3960989 ACTTTGTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:3961530 original size:7 final size:7
Alignment explanation
Indices: 3961520--3961544 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3961510 TAAATTATAA
3961520 AAAAGTT
1 AAAAGTT
3961527 AAAAGTT
1 AAAAGTT
3961534 AAAAGTT
1 AAAAGTT
3961541 AAAA
1 AAAA
3961545 ATTTATGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (7 bp):
AAAAGTT
Found at i:3962709 original size:23 final size:23
Alignment explanation
Indices: 3962682--3962727 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3962672 ATGTTGAAAG
3962682 TTAACTTTTTTTAAATCATTATT
1 TTAACTTTTTTTAAATCATTATT
3962705 TTAACTTTTTTTAAATCATTATT
1 TTAACTTTTTTTAAATCATTATT
3962728 AAGTTGACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (23 bp):
TTAACTTTTTTTAAATCATTATT
Found at i:3966329 original size:6 final size:6
Alignment explanation
Indices: 3966318--3966344 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3966308 CTTTTTTAAG
3966318 TTCTAC TTCTAC TTCTAC TTCTAC TTC
1 TTCTAC TTCTAC TTCTAC TTCTAC TTC
3966345 ATTTTTGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.52
Consensus pattern (6 bp):
TTCTAC
Found at i:3966611 original size:21 final size:19
Alignment explanation
Indices: 3966587--3966630 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
3966577 TCTAATTTTG
3966587 TTTTTATTATTTCCTGGTTT
1 TTTTTATTATTTCCT-GTTT
* *
3966607 CTTTTTTTTTTTTCCTGTTT
1 -TTTTTATTATTTCCTGTTT
3966627 TTTT
1 TTTT
3966631 CTAATAATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 4 0.19
21 13 0.62
ACGTcount: A:0.05, C:0.11, G:0.07, T:0.77
Consensus pattern (19 bp):
TTTTTATTATTTCCTGTTT
Done.